Spatial atlas of the mouse central nervous system at molecular resolution

Abstract Spatially charting molecular cell types at single-cell resolution across the 3D volume is critical for illustrating the molecular basis of brain anatomy and functions. Single-cell RNA sequencing has profiled molecular cell types in the mouse brain 1,2 , but cannot capture their spatial organization. Here we used an in situ sequencing method, STARmap PLUS 3,4 , to profile 1,022 genes in 3D at a voxel size of 194 × 194 × 345 nm 3 , mapping 1.09 million high-quality cells across the adult mouse brain and spinal cord. We developed computational pipelines to segment, cluster and annotate 230 molecular cell types by single-cell gene expression and 106 molecular tissue regions by spatial niche gene…